The Future of Genomic Compression
Save Terabytes with Genozip

Example of compressing paired-end FASTQ files. These are Illumina NovaSeq 30X WGS files:

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[20:23:56]$ genozip sample_R1.fastq.gz sample_R2.fastq.gz --pair --reference GRCh38.fa
genozip sample_R1.fastq.gz : Done (2 minutes 50 seconds)
genozip sample_R2.fastq.gz : Done (6 minutes 30 seconds, FASTQ compression ratio: 21.8 - better than .fastq.gz by a factor of 4.5)
testing: genounzip sample_R1.fastq.gz : verified as identical to the original FASTQ
testing: genounzip sample_R2.fastq.gz : verified as identical to the original FASTQ

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[20:35:06]$ ls -nh *fastq*
-rw-------+ 1 100 100 29G Oct 12  2020 sample_R1.fastq.gz
-rw-------+ 1 100 100 33G Oct 12  2020 sample_R2.fastq.gz

-rw-------+ 1 100 100 14G Jan 12 20:33 sample_R1+2.fastq.genozip

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Example of compressing a BAM file. This is the same NovaSeq data as above, aligned with bwa mem:

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[20:56:02]$ genozip sample.bam --reference GRCh38.fa
genozip sample.bam : Done (11 minutes 26 seconds, BAM compression ratio: 3.8)
testing: genounzip sample.bam.genozip : verified as identical to the original BAM

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[21:20:02]$  ls -nh sample.bam*
-rw-------+ 1 100 100 56G Apr 10  2022 sample.bam
-rw-------+ 1 100 100 15G Jan 12 21:07 sample.bam.genozip

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Example of compressing a VCF file. This is a GVCF file generated with GATK HaplotypeCaller and GenotypeGVCFs

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[19:39:02]$ genozip sample.g.vcf.gz --reference GRCh38.fa

genozip sample.g.vcf.gz : Done (6 minutes 33 seconds, VCF compression ratio: 202.2 - better than .vcf.gz by a factor of 15.5)

testing: genounzip sample.g.vcf.genozip : verified as identical to the original VCF
 

[19:54:23 $] ls -nh sample.g.vcf.*

-rw-rw-r--+ 1 100 100 13G  May 13  2020 sample.g.vcf.gz

-rw-rw-r--+ 1 100 100 838M May 11 19:45 sample.g.vcf.genozip

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